Interpretive Summary: Many agricultural producers are interested in implementing alternative crop systems, and information to understand effects of alternative systems on water quality is needed. Also, while it is known that nutrient losses beneath perennial crops can be a fraction of losses observed under row crops, there is a need to document what benefit may occur from crop systems that include annual row crops and perennial forages. This study compared nitrate and total phosphorus concentrations in soil water beneath three different cropping systems suitable for the U.S. Midwest: a two-year corn-soybean rotation, a three-year corn-soybean small grain/red clover system, and a four-year corn-soybean-small grain/alfalfa-alfalfa system. Nutrient applications were made in spring and were managed carefully with rates based on soil testing. Synthetic fertilizers were used in the two-year rotation, whereas composted manure, legume residues, and low amounts of synthetic fertilizers provided nutrients in the three- and four-year systems. After eight years of monitoring, the four-year system, particularly during the alfalfa and following corn years, had smaller concentrations of nitrate-N and lower frequency of total phosphorus detection in soil water. For nitrate-N, seasonal patterns were found among systems that could be explained based on cycling of nitrogen in soil and crop residue decomposition. It is often assumed that water quality tradeoffs between nitrate and phosphorus losses are ubiquitous, but this study shows cropping systems that include alfalfa and use soil testing to determine nutrient applications a can reduce the loss of both nutrients. Results are of interest to agricultural producers and the conservation community, who are seeking approaches to manage the impacts of both nitrogen and phosphorus on surface water quality.

Technical Abstract:
tSubsurface nutrient losses differ between annual and perennial crops; however, nutrient losses fromcropping systems that rotate annual and perennial crops are poorly documented. This study trackedNO3-N and P in soil water under three cropping systems suited for the U.S. Midwest, includingtwo-year (corn–soybean; 2YS), three-year (corn–soybean–small grain/red clover; 3YS), and four-year(corn–soybean–small grain/alfalfa–alfalfa; 4YS) systems. Nutrient applications were based on soil-testresults, and solely comprised inorganic fertilizers to 2YS corn, whereas, in the 3YS and 4YS systems, nutri-ents were provided by legume residues, and a managed balance of composted manure, and inorganicfertilizers. Soil water was collected from 2004 through 2011 using suction samplers. The 4YS system hadsmaller concentrations of NO3-N and a lower frequency of P detection (p < 0.05) during the establishedalfalfa and subsequent corn crop than other crop-years in the experiment. Mean concentrations of NO3-Nwere 1.1 mg NO3-N L-1under alfalfa and 6.5 mg NO3-N L-1under the following 4YS corn crop, comparedto average concentrations between 8.7 and 18.1 mg NO3-N L-1among all other crop-years. Seasonal NO3-N dynamics among the three systems were explainable based on mineralization and – immobilizationof N from decomposing crop residues. Large P concentrations (0.23–1.02 mg P L-1) occurred in one plotthat occasionally ponded, indicating P transport to depth by preferential flow is a risk in some soils onthis landscape. Among the remaining plots, the proportion of samples with detectable P concentrations(i.e., >0.02 mg L-1) was less (p < 0.05) under the 4YS system (0.26) than observed for the experiment over-all (0.35), which resulted from infrequent detection (0.17) of P in soil water during the alfalfa and corncrops. Results provide evidence that rotational systems including alfalfa with annual crops and use of soiltesting in nutrient management can reduce movement of N and P below the root zone.